On Fri, Mar 7, 2008 at 5:04 PM, DeLano Scientific <del...@delsci.info> wrote: > So from where I sit, the obvious open-source candidates are: > > APBS (electrostatics -- improve the current plugin)
Please let me know if anyone decides to do this. I have an (unreleased) improved version, and several ideas for how to improve it further. I'd be glad to help out. -michael > RDKit (cheminformatics, depiction, UFF cleanup, etc.) > mengine (MMFF small molecule cleanup) > mpeg_encode (MPEG movie production on Linux, etc.) > GIMP (image manipulation) > Blender (general-purpose 3D modeling & animation) > Jmol (publishing visualizations inside of web pages) > Firefox (ditto) > MMTK (molecular mechanics -- Python/flexible) > GROMACS (molecular mechanics -- C/fast) > OpenOffice (escape from the microsoft hegemony) > > (NOTE: work is already underway for mpeg_encode and mengine...) > > Are there other key open-source packages we might specifically target for > integration with PyMOL, either through SOC or beyond? > > Although there are many niche tools, from a prioritization standpoint, > efforts should focus on integrations that will impact the largest potential > user base. So what hypothetical integrations would be useful to virtually > all medicinal chemists, all structural biologists, all movie-makers, all > paper-writers, and so on? > > Cheers, > Warren > > -- > DeLano Scientific LLC > Subscriber Support Services > mailto:del...@delsci.info > > > > > > -----Original Message----- > > From: Anders Norgaard [mailto:anders.norga...@gmail.com] > > Sent: Wednesday, March 05, 2008 1:10 PM > > To: DeLano Scientific > > Cc: pymol-users@lists.sourceforge.net > > Subject: Re: [PyMOL] Will Pymol participate in Google Summer > > of Code 2008? > > > > On Wed, Mar 5, 2008 at 9:57 PM, DeLano Scientific > > <del...@delsci.info> wrote: > > > Anders, > > > > > > No plans at present, but hey, it is still one whole week before a > > > week before the deadline! > > > > :o) > > > > > Anyone out there with sufficient bandwidth to mentor? > > > Hmm... Perhaps a nucleating effort on Jmol / PyMOL interporability > > > would make a good SOC project? > > > > Well, there is also a whole list of stuff in your "PyMOL "By > > Popular Demand" Survey (Jan 2008)" mail, perhaps some of > > these could be bundled into a project? > > > > - An ActiveX Control > > - 2D structure display > > - More documentation, screencasts, & tutorials. > > - Browser plugins > > - Direct MPEG movie export > > - Direct WinAVI movie export > > - Structure cleanup & energy minimization > > - Objects/states split over multiple windows (side by side views) > > - Multi-line text annotations in scenes > > - APBS bundled witih PyMOL > > - Per-object Z clip > > - "native" Windows user interface in a single window > > - Undo > > - Improved molecular builder > > - Better RigiMOL integration > > - MOPAC integration > > - Sequence alignment editing > > - 3D PDF export > > - Cleaned up matrix & transformation interface > > - Blender integration > > - Nucleic acid building > > - Calculate surface areas and volumes > > - Secondary structure display in sequence viewer > > - Scene buttons / sorter > > - Movie "slider" ala Cinema4D/Maya/3DSMax > > - Drag & drop programming of object motions > > > > or > > > > Pymol MMTK integration? > > > > > > Best, > > Anders > > > > > > > > > > > > > > Cheers, > > > Warren > > > > > > > > > > > > > -----Original Message----- > > > > From: pymol-users-boun...@lists.sourceforge.net > > > > [mailto:pymol-users-boun...@lists.sourceforge.net] On > > Behalf > Of > > > Anders Norgaard > Sent: Wednesday, March 05, 2008 8:53 AM > To: > > > pymol-users@lists.sourceforge.net > Subject: [PyMOL] Will Pymol > > > participate in Google Summer of Code 2008? > > > > > > > > Hi, > > > > > > > > > > > > I guess that it is one of the great ways to catch young new > > > > contributors. > > > > > > > > http://code.google.com/soc/2008/ > > > > > > > > > > > > Best, > > > > Anders > > > > > > > > -------------------------------------------------------------- > > > > ----------- > > > > This SF.net email is sponsored by: Microsoft Defy all > > > > challenges. Microsoft(R) Visual Studio 2008. > > > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > > > _______________________________________________ > > > > PyMOL-users mailing list > > > > PyMOL-users@lists.sourceforge.net > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909 http://www.umich.edu/~mlerner
